Until recently, fluoroquinolones (FQs) have been the preferred agents for treating multiple types of bacterial infection, including urinary tract infections (UTIs), most of which are caused by Escherichia coli. FQ resistance, however, is increasingly prevalent in E. coli, leading the 2010 Infectious Diseases Society of America guidelines to recommend nitrofurantoin over FQs for empirical treatment of uncomplicated UTI (See, e.g. Gupta K, Hooton T M, Naber K G, et al. International Clinical Practice Guidelines for the Treatment of Acute Uncomplicated Cystitis and Pyelonephritis in Women: A 2010 Update by the Infectious Diseases Society of America and the European Society for Microbiology and Infectious Diseases. Clin. Infect Dis. 2011; 52:e103-e20), allowing some patients to progress to severe illness or death despite receipt of conventional empirical therapy (See, e.g., Owens R C, Johnson J R, Stogstill P, Yarmus L, Lolans K, Quinn J. Community Transmission in the United States of a CTX-M-15-Producing Sequence Type ST131 Escherichia coli Strain Resulting in Death. J. Clin. Microbiol. 2011; 49:3406-8).
In E. coli, although reduced FQ susceptibility may result from up-regulated efflux pumps and plasmid-regulated resistance mechanisms, high-level FQ resistance typically requires 1-2 point mutations within the quinolone resistance-determining regions (QRDRs) of both gyrA and parC, the chromosomal genes encoding the FQ targets DNA gyrase and topoisomerase IV, respectively. This has been shown, for example, in Hooper (2000) (Hooper D C., Mechanisms of action and resistance of older and newer fluoroquinolones. Clin. Infect. Dis. 2000; 31 (Suppl 2):S24-S8) and Hooper (2001) (Hooper D C. Emerging mechanisms of fluoroquinolone resistance. Emerg. Infect. Dis. 2001; 7:337-41). Because of its chromosomal basis, such FQ resistance has arisen in diverse E. coli clonal lineages, all of which presumably acquired QRDR mutations independently (See, e.g. Johnson J R, et al. Epidemic clonal groups of Escherichia coli as a cause of antimicrobial-resistant urinary tract infections in Canada, 2002-2004. Antimicrob Agents Chemother 2009; 53:2733-9; Cagnacci S, et al. European emergence of ciprofloxacin-resistant Escherichia coli clonal groups O25:H4-ST 131 and O15:K52:H1 causing community-acquired uncomplicated cystitis. J Clin Microbiol 2008; 46(8):2605-12; and Johnson J R, et al. Escherichia coli sequence type ST131 as the major cause of serious multidrug-resistant E. coli infections in the United States (2007). Clin Infect Dis 2010; 51:286-94).
Despite the high clonal diversity of FQ-R strains, the past decade has seen the rapid emergence and global spread of a specific FQ-resistance-associated E. coli lineage, ST131, one of ≧1000 E. coli sequence types (STs), as defined by multi-locus sequence typing (MLST). However, it has been unknown whether ST131's association with FQ resistance is due to the frequent, independent emergence of resistance in different strains or, instead, expansion of a single resistant strain. Such sub-ST analysis is critical to the development of epidemiologic and clinical measures to address the ongoing emergence of FQ-resistant (FQ-R) E. coli. 
The excess risk associated with the ST131 lineage was described in a number of previous publications.
Currently, there are a number of E. coli detection assays but they are either for general species confirmation or for identification of pathogenic lineages unrelated to FQ-resistance. Although assays exist for the detection of ST131, they do not differentiate between the most important sub-clones of ST131, H30-R and H30-Rx (as described below) and other ST131 sub-clones. There is a need for a kit, assay, and methods for detecting the presence of this high-risk sub-clones of E. coli. 